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529 add ncbi biosample and project ids to neon soil #354
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mbthornton-lbl
merged 10 commits into
main
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529_add_NCBI_biosample_and_project_ids_to_NEON_soil
Nov 15, 2023
Merged
529 add ncbi biosample and project ids to neon soil #354
mbthornton-lbl
merged 10 commits into
main
from
529_add_NCBI_biosample_and_project_ids_to_NEON_soil
Nov 15, 2023
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pkalita-lbl
previously approved these changes
Nov 6, 2023
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Overall looks good. Two non-critical comments:
- I guess I'm not fully up-to-speed on what the api-napa instance is, but I'm a little confused about the code that sort of uses that term interchangeably with "dev instance". To me "dev" is what's deployed on
api-dev.microbiomedata.org
. It might make more sense to me to remove theget_runtime_client
method and the--use_dev_api
flag, and let it all be driven by environment variables. Want to use the api-napa instance? Okay, then set yourAPI_HOST
envar accordingly. That's just my outsider view of how I'd expect something like this to work. If that doesn't make sense to you, forget I said anything. - It doesn't look like
python-dotenv
is listed inmain.in
but we get it as a transitive dependency of other stuff. If we're using it directly we should list it as a direct dependency.
pkalita-lbl
previously approved these changes
Nov 14, 2023
pkalita-lbl
approved these changes
Nov 15, 2023
mbthornton-lbl
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November 15, 2023 22:48
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This PR provides:
A python script to:
Note: Validation was performed against the api-napa instance, dev and prod as of Nov 3 blocked by:
#350
Minor updates to simplify setup and some of the methods on the runtime API client.
Output Changefile:
https://drive.google.com/file/d/1bqBgUI8YfQT5ho0Lz02E2mzfCsaBKt-t/view?usp=drive_link